Structure of PDB 6vjs Chain D

Receptor sequence
>6vjsD (length=1164) Species: 562 (Escherichia coli) [Search protein sequence]
LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLF
CARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIEL
ASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQ
QILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNE
TNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDG
GRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALL
DNGRRGRAITGSNKRPLKSLADMIKGKQRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWD
ILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNAD
FDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGL
YYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDAN
GELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYR
ILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRD
GQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPIT
ANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVT
EDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPR
NTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIIN
KGEAIGVIAAQSIGEPGTQLTDITGGLPRVADLFEARRPKEPAILAEISG
IVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVIS
DGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQML
RKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITK
ASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGT
GYAYHQDRMRRRAA
3D structure
PDB6vjs Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus -Based Wound Infection Model in SKH1 Mice.
ChainD
Resolution4.02 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 QZY D I331 G344 K345 I1320 A1323 S1324 L1332 V1351 I1352 I324 G334 K335 I1109 A1112 S1113 L1121 V1140 I1141
BS02 ZN D C70 C85 C63 C78
BS03 ZN D C888 C895 C898 C878 C885 C888
BS04 MG D D460 D462 D464 D450 D452 D454
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006879 intracellular iron ion homeostasis
GO:0009408 response to heat
GO:0031564 transcription antitermination
GO:0032784 regulation of DNA-templated transcription elongation
GO:0036460 cellular response to cell envelope stress
GO:0042128 nitrate assimilation
GO:0044780 bacterial-type flagellum assembly
GO:0046677 response to antibiotic
GO:0048870 cell motility
GO:0071973 bacterial-type flagellum-dependent cell motility
GO:0090605 submerged biofilm formation
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0008023 transcription elongation factor complex
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vjs, PDBe:6vjs, PDBj:6vjs
PDBsum6vjs
PubMed32886885
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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